Previous changeset 1:92e77800ef2c (2024-02-09) Next changeset 3:c35e0075c7a2 (2024-12-03) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b |
modified:
macros.xml phyloseq_from_dada2.R test-data/output.phyloseq test-data/sequence_table.dada2_sequencetable |
added:
phyloseq_from_biom.R test-data/biom-refseq.fasta test-data/biom-tree.phy test-data/rich_dense_otu_table.biom test-data/rich_dense_otu_table.biom2 test-data/sample_data.tabular |
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diff -r 92e77800ef2c -r dfe800a3faaf macros.xml --- a/macros.xml Fri Feb 09 21:42:09 2024 +0000 +++ b/macros.xml Sat Mar 16 07:56:05 2024 +0000 |
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@@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.38.0</token> + <token name="@TOOL_VERSION@">1.46.0</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.01</token> <xml name="bio_tools"> @@ -10,8 +10,8 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-phyloseq</requirement> - <requirement type="package" version="1.7.1">r-optparse</requirement> - <requirement type="package" version="1.3.1">r-tidyverse</requirement> + <requirement type="package" version="1.7.3">r-optparse</requirement> + <requirement type="package" version="2.0.0">r-tidyverse</requirement> </requirements> </xml> <xml name="phyloseq_input"> |
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diff -r 92e77800ef2c -r dfe800a3faaf phyloseq_from_biom.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_from_biom.R Sat Mar 16 07:56:05 2024 +0000 |
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@@ -0,0 +1,30 @@ +#!/usr/bin/env Rscript + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("phyloseq")) +suppressPackageStartupMessages(library("tidyverse")) + +option_list <- list( + make_option(c("--BIOMfilename"), action = "store", dest = "biom", help = "Input BIOM file"), + make_option(c("--treefilename"), action = "store", dest = "tree", default = NULL, help = "Input Tree newick/nexus file"), + make_option(c("--parseFunction"), action = "store", dest = "parsefoo", default = "parse_taxonomy_default", help = "Parse function parse_taxonomy_default/read_tree_greengenes"), + make_option(c("--refseqfilename"), action = "store", dest = "sequences", default = NULL, help = "Input Sequence fasta file"), + make_option(c("--output"), action = "store", dest = "output", help = "RDS output") +) + +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) +args <- parse_args(parser, positional_arguments = TRUE) +opt <- args$options + +parsefoo <- get(opt$parsefoo) +phyloseq_obj <- import_biom( + BIOMfilename = opt$biom, + treefilename = opt$tree, + refseqfilename = opt$sequences, + parseFunction = parsefoo +) + +print(phyloseq_obj) + +# save R object to file +saveRDS(phyloseq_obj, file = opt$output, compress = TRUE) |
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diff -r 92e77800ef2c -r dfe800a3faaf phyloseq_from_dada2.R --- a/phyloseq_from_dada2.R Fri Feb 09 21:42:09 2024 +0000 +++ b/phyloseq_from_dada2.R Sat Mar 16 07:56:05 2024 +0000 |
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@@ -7,6 +7,7 @@ option_list <- list( make_option(c("--sequence_table"), action = "store", dest = "sequence_table", help = "Input sequence table"), make_option(c("--taxonomy_table"), action = "store", dest = "taxonomy_table", help = "Input taxonomy table"), + make_option(c("--sample_table"), action = "store", default = NULL, dest = "sample_table", help = "Input sample table"), make_option(c("--output"), action = "store", dest = "output", help = "RDS output") ) @@ -15,20 +16,40 @@ opt <- args$options # The input sequence_table is an integer matrix # stored as tabular (rows = samples, columns = ASVs). -seq_table_numeric_matrix <- data.matrix(read.table(opt$sequence_table, sep = "\t")) +seq_table_numeric_matrix <- data.matrix(read.table(opt$sequence_table, header = T, sep = "\t", row.names = 1, check.names = FALSE)) # The input taxonomy_table is a table containing # the assigned taxonomies exceeding the minBoot # level of bootstrapping confidence. Rows correspond # to sequences, columns to taxonomic levels. NA # indicates that the sequence was not consistently # classified at that level at the minBoot threshold. -tax_table_matrix <- as.matrix(read.table(opt$taxonomy_table, header = FALSE, sep = "\t")) +tax_table_matrix <- as.matrix(read.table(opt$taxonomy_table, header = T, sep = "\t", row.names = 1, check.names = FALSE)) # Construct a tax_table object. The rownames of # tax_tab must match the OTU names (taxa_names) # of the otu_table defined below. tax_tab <- tax_table(tax_table_matrix) + # Construct an otu_table object. otu_tab <- otu_table(seq_table_numeric_matrix, taxa_are_rows = TRUE) + # Construct a phyloseq object. phyloseq_obj <- phyloseq(otu_tab, tax_tab) +if (!is.null(opt$sample_table)) { + sample_tab <- sample_data( + read.table(opt$sample_table, header = T, sep = "\t", row.names = 1, check.names = FALSE) + ) + phyloseq_obj <- merge_phyloseq(phyloseq_obj, sample_tab) +} + +# use short names for our ASVs and save the ASV sequences +# refseq slot of the phyloseq object as described in +# https://benjjneb.github.io/dada2/tutorial.html +dna <- Biostrings::DNAStringSet(taxa_names(phyloseq_obj)) +names(dna) <- taxa_names(phyloseq_obj) +phyloseq_obj <- merge_phyloseq(phyloseq_obj, dna) +taxa_names(phyloseq_obj) <- paste0("ASV", seq(ntaxa(phyloseq_obj))) + +print(phyloseq_obj) + +# save R object to file saveRDS(phyloseq_obj, file = opt$output, compress = TRUE) |
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diff -r 92e77800ef2c -r dfe800a3faaf test-data/biom-refseq.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biom-refseq.fasta Sat Mar 16 07:56:05 2024 +0000 |
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@@ -0,0 +1,29 @@ +>GG_OTU_1 +AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCA +TGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCCGTGTAGCGGTG +AAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTG +GGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGATTACTAGGTGTGGGGGTCTGACCCCTTCCGT +GCCGGAGTTAACAC +>GG_OTU_2 +TACGTAGGGAGCAAGCGTTATCCGGATTTATTGGGTGTAAAGGGTGCGTAGACGGGAGAACAAGTTAGTTGTGAAAGCCC +TCGGCTTAACTGAGGAACTGCAACTAAAACTATTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTG +AAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGTTGAGGCACGAAAGTGTG +GGGAGCAAACAGGATTAGATACCCTGGTAGTCCACACCGTAAACGATGGATACTAGGTGTAGGAGATGATTTCATCATCT +GTGCCGAAAGCAAACGCAATAAGTATCCCACCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGATTGACGGGGCCCG +CACAAGCAGTGGAGTATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGGCTTGACATA +>GG_OTU_3 +TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATCACAAGTCAGAAGTGAAAAATC +CGGGGGCTCCAACCCCGGAACTGCTTTTGAAACTGTGGAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCG +GTAGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGC +GTGGGGAGC +>GG_OTU_4 +TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCC +GGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGTCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTG +AAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATAACTGACGCTGAGGCTCGAAAGCGTG +GGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATACTAGGTGTTGGGAAGCATTGCTTCTCGGT +GCCGTCGCAAACGCAGTAAGTATTCCACCTGGGGGATACGTTTCGACAAGAATAGAAACTACAAAAGGAATTAGGACGGG +GACCCGCACAAGCGGTGAGCATGTGGTTAATCGAAGCAACGCGAAGAACCTTA +>GG_OTU_5 +AACGTAGGGTGCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGACAAGTTGGAAGTGAAACCATG +GGCTCAACCCATGAATTGCTTTCAAAACTGTTTTTCTTGAGTTAGTGCAGAGGTAGATGGAATTCCCGGTGTAGCGGTGG +AATGCGTAGATATCGGGA |
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diff -r 92e77800ef2c -r dfe800a3faaf test-data/biom-tree.phy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biom-tree.phy Sat Mar 16 07:56:05 2024 +0000 |
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@@ -0,0 +1,1 @@ +(((GG_OTU_1:0.00892,GG_OTU_2:0.01408)1.000.2:0.12196,GG_OTU_3:0.16022)0.995.2:0.01869,(GG_OTU_4:0.08976,GG_OTU_5:0.0665)0.766:0.09714)0.764.3; |
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diff -r 92e77800ef2c -r dfe800a3faaf test-data/output.phyloseq |
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Binary file test-data/output.phyloseq has changed |
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diff -r 92e77800ef2c -r dfe800a3faaf test-data/rich_dense_otu_table.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rich_dense_otu_table.biom Sat Mar 16 07:56:05 2024 +0000 |
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@@ -0,0 +1,56 @@ +{ + "id":null, + "format": "Biological Observation Matrix 1.0.0-dev", + "format_url": "http://biom-format.org", + "type": "OTU table", + "generated_by": "QIIME revision XYZ", + "date": "2011-12-19T19:00:00", + "rows":[ + {"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}, + {"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}}, + {"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__"]}}, + {"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}}, + {"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}} + ], + "columns":[ + {"id":"Sample1", "metadata":{ + "BarcodeSequence":"CGCTTATCGAGA", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample2", "metadata":{ + "BarcodeSequence":"CATACCAGTAGC", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample3", "metadata":{ + "BarcodeSequence":"CTCTCTACCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample4", "metadata":{ + "BarcodeSequence":"CTCTCGGCCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample5", "metadata":{ + "BarcodeSequence":"CTCTCTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample6", "metadata":{ + "BarcodeSequence":"CTAACTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}} + ], + "matrix_type": "dense", + "matrix_element_type": "int", + "shape": [5,6], + "data": [[0,0,1,0,0,0], + [5,1,0,2,3,1], + [0,0,1,4,2,0], + [2,1,1,0,0,1], + [0,1,1,0,0,0]] + } + |
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diff -r 92e77800ef2c -r dfe800a3faaf test-data/rich_dense_otu_table.biom2 |
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Binary file test-data/rich_dense_otu_table.biom2 has changed |
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diff -r 92e77800ef2c -r dfe800a3faaf test-data/sample_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_data.tabular Sat Mar 16 07:56:05 2024 +0000 |
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@@ -0,0 +1,3 @@ + Property Number +SRR14190457 Early 1 +SRR14190458 Late 2 \ No newline at end of file |
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diff -r 92e77800ef2c -r dfe800a3faaf test-data/sequence_table.dada2_sequencetable --- a/test-data/sequence_table.dada2_sequencetable Fri Feb 09 21:42:09 2024 +0000 +++ b/test-data/sequence_table.dada2_sequencetable Sat Mar 16 07:56:05 2024 +0000 |
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b'@@ -1,65 +1,65 @@\n-\tSRR14190457\n-GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGAAACCCCCGTAGTCC\t178\n-GTGTCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACTGGTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGTCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGGATTAGAAACCCCCGTAGTCC\t136\n-GTGTCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGAAACCCCAGTAGTCC\t129\n-GTGTCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCCCGTAGTCC\t128\n-GTGTCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTGTGTAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTATGTAACTAGAGTGTCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATCACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGCGTAGTCC\t110\n-GTGTCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCCCGTAGTCC\t104\n-GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAAGATAAGTCTGATGTGAAAGCCCCCGGCTTAACCGAGGAATTGCATCGGAAACTGTGTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGATACCCCCGTAGTCC\t97\n-GTGTCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCCGTAGTCC\t90\n-GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTCCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGAAACCCCAGTAGTCC\t88\n-GTGTCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCCGTAGTCC\t86\n-GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAAGATAAGTCTGATGTGAAAGCCCCCGGCTTAACCGAGGAATTGCATCGGAAACTGTGTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGAAACCCCCGTAGTCC\t84\n-GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAAAATAAGTCTAATGTGAAAGCCCTCGGCTTAACCGAGGAACTGCATCGGAAACTGTTTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGAAACCCCCGTAGTCC\t83\n-GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGAAACCCCAGTAGTCC\t71\n-GTGTCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGAGTGGCAAGTCTGATGTGAAAACCC'..b'CAGTGGCGAAGGCGGATAACTGGACGGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCTTGTAGTCC\t28\t71\n+GTGTCAGCAGCCGCGGTAAAACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAAGCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGTAGCGAACGGGATTAGATACCCCCGTAGTCC\t28\t71\n+GTGTCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATGGACAAGTCTGATGTGAAAGGCTGGGGCTCAACCCCGGGACTGCATTGGAAACTGCCCGTCTTGAGTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATCACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCGCGTAGTCC\t27\t83\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGCTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCGATGGCGAAGGCAGGTCTCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGAAACCCCCGTAGTCC\t27\t84\n+GTGTCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCTGGGGCTTAACTCCGGGCGTGCAGGCGATACGGGCATAACTTGAGTGCTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCGAACAGGATTAGATACCCCAGTAGTCC\t26\t86\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAAGATAAGTCTGATGTGAAAGCCCCCGGCTTAACCGAGGAATTGCATCGGAAACTGTGTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGATACCCTAGTAGTCC\t26\t88\n+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCCGTAGTCC\t25\t90\n+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCTTGTAGTCC\t24\t97\n+GTGTCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCAAAACTACTGAGCTAGAGTACGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCGCGTAGTCC\t22\t104\n+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCCCGTAGTCC\t22\t110\n+GTGTCAGCAGCCGCGGTAATACGTAGGGGGCTAGCGTTATCCGGAATTACTGGGCGTAAAGGGTGCGTAGGTGGTTTCTTAAGTCAGAGGTGAAAGGCTACGGCTCAACCGTAGTAAGCCTTTGAAACTGAGAAACTTGAGTGCAGGAGAGGAGAGTAGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAATACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGCGTAGTCC\t22\t128\n+GTGTCAGCAGCCGCGGTGATACGTAGGGTGCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGTGGTTGATCGCGTCGGAAGTGTAATCTTGGGGCTTAACCCTGAGCGTGCTTTCGATACGGGTTGACTTGAGGAAGGTAGGGGAGAATGGAATTCCTGGTGGAGCGGTGGAATGCGCAGATATCAGGAGGAACACCAGTGGCGAAGGCGGTTCTCTGGGCCTTTCCTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGCTTAGATACCCCTGTAGTCC\t16\t129\n+GTGTCAGCAGCCGCGGTAATACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGACTGTCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGCGGTCTTGAGTGAGCGAGAAGTACGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCGTACCGGCGCTCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGGATTAGATACCCCCGTAGTCC\t15\t136\n+GTGTCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTATCCGGATTCACTGGGTTTAAAGGGTGCGTAGGCGGGCGTATAAGTCAGTGGTGAAATCCTGGAGCTTAACTCCAGAACTGCCATTGATACTATATGTCTTGAATATGGTGGAGGTAAGCGGAATATGTCATGTAGCGGTGAAATGCATAGATATGACATAGAACACCTATTGCGAAGGCAGCTTACTACGCCTATATTGACGCTGAGGCACGAAAGCGTGGGGATCAAACAGGATTAGAAACCCGAGTAGTCC\t11\t178\n' 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